They were tightened in the sequence that you stated

 

Could be driveshaft, may have been masked by the motor mounts? IDK just a guess, could try rotating it to see if that does anything

 

I've had the pinion nut on my diff come loose, not sure how. that caused a vibration for me.

 

OEM mounts are soft, meant to absorb the most vibration possible for comfort and noise reduction. I dont know about the OP mounts specifically, but generally when you move to an aftermarket performance style, you get the benefit of less drivtrain movement for more response and power to the ground, but they will transmit more vibration through the chassis, and will also magnify any pre existing issue thats happening somewhere in the drivetrain, including wheel balance. Good luck in the search.

 

Transmission casing was cracked y'all. It actually completely cracked all the way around. I'm in the process of fixing this now then hopefullly that'll solve the vibration issue. If not I'll just assume that the case broke due to the excessive vibration and my issue is still out there. I'll be checking to see if the drive shaft is properly balanced.